A full sib mating design was used to select for increased perithecial number in matings between sexually compatible pairs of ascospore progeny of the fungus Cochliobolus heterostrophus. In the third generation of selection approximately one-half of the isolate pairs produced abnormally low numbers of perithecia, indicating segregation at a single locus controlling fertility, which was independent of the mating type locus. We termed the phenomenon secondary sexual incompatibility, although it may also be related to vegetative compatibility. Large numbers of perithecia formed when the paired sexually compatible isolates had different alleles at the locus; few formed when they had identical alleles. Additional studies of two full sib families from another population showed the presence of at least four loci that condition secondary sexual incompatibility among these isolates. High fertility occurred only between isolates with different alleles at least one of the four loci. This phenomenon appears similar to the enhancement of fertility in Ceratocystis ulmi by genes for heterokaryon incompatibility, but the relationship of secondary sexual incompatibility loci to heterokaryon incompatibility loci in C. heterostrophys has not been determined.